@cruis
HO do not dig into that deep as the way you have explained, they are more concern that your tax return reflect's the points that you are claiming, in you case you only needed 35k and your SA302 does reflect this. But any way you have done the amendment it's good if situation do come to your initial tax returns than at-least you can say explains yourself and also show them that you have rectify your mistake/error way before your ILR.
Also please don't got to PEO but go for postal application and please do not add any SA302 or Self-Assessment Document in your postal file, keep it simple and hope for the best, if they wanted to check HMRC record, they can check it any ways as they have access to HMRC Data. So No Point of Sending these additional document's.
Why any one want to add these additional documents ? Why ? Have the ask about it ?
If you look into the recent trend the only people that had being called for the interview are the one who have send the Self-Assessment document e.g. like revise tax calculation or Account Letter explaining the tax discrepancy. Also cases where in past they manage to earn let say 15,000 in 3 months just before the initial or extension application's with made up invoices and the rest of year it's all nill business as per HMRC, such situation do raise concern with HO and this was the main reason that Tier 1 - General was Close.
lastly if you have used TOIEC in past than except a call for the interview
Keep it Simple!!! Best Advice Looking at the Current Situation.